Code
library(knitr)
library(targets)
library(MiscMetabar)Where we see the pipeline processes
Date: October 19, 2024
library(knitr)
library(targets)
library(MiscMetabar)tar_glimpse(script=here::here("_targets.R"), targets_only = TRUE, callr_arguments = list(show = FALSE))#d_pq <- tar_read(script=here::here("_targets.R"))
d_pq <- data_fungiThe {targets} package is at the core of this project. Please read the intro of the user manual if you don’t know {targets}.
The {targets} package store … targets in a folder and can load (tar_load()) and read (tar_read) object from this folder.
DT::datatable(d_pq@sam_data)formattable_pq(
d_pq,
"Height",
min_nb_seq_taxa = 10000,
formattable_args = list("Phylum" = FALSE),
log10trans = TRUE
)54 samples were discarded due to NA in variable modality
Cleaning suppress 0 taxa ( ) and 22 sample(s) ( BE9-006-B_S27_MERGED.fastq.gz / BG7-010-H_S31_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / D9-027-B_S83_MERGED.fastq.gz / DJ2-008-B_S87_MERGED.fastq.gz / DJ2-008-H_S88_MERGED.fastq.gz / DY5-004-H_S97_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / E9-009-H_S101_MERGED.fastq.gz / J18-004-B_S114_MERGED.fastq.gz / J18-004-H_S115_MERGED.fastq.gz / J18-004-M_S116_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / O20-X-B_S139_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / R28-008-H_S159_MERGED.fastq.gz / R28-008-M_S160_MERGED.fastq.gz / W26-001-H_S166_MERGED.fastq.gz / W26-001-M_S167_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
Number of non-matching ASV 0
Number of matching ASV 1420
Number of filtered-out ASV 1400
Number of kept ASV 20
Number of kept samples 109
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(OTU)`
| OTU | Order | Family | Genus | High | Low | Middle | proportion_samp | nb_seq |
|---|---|---|---|---|---|---|---|---|
| ASV2 | Xylariales | Diatrypaceae | Eutypa | 4.43 | 4.78 | 3.65 | 0.74 | 4.97 |
| ASV6 | Xylariales | Xylariaceae | Xylaria | 4.51 | 4.00 | 3.69 | 0.14 | 4.73 |
| ASV7 | Russulales | Stereaceae | NA | 4.20 | 3.58 | 3.81 | 0.24 | 4.68 |
| ASV8 | Russulales | Stereaceae | Stereum | 4.16 | 3.52 | 4.08 | 0.50 | 4.67 |
| ASV10 | NA | NA | NA | 4.43 | 3.07 | 3.73 | 0.26 | 4.61 |
| ASV12 | Hymenochaetales | Schizoporaceae | Xylodon | 3.26 | 3.91 | 3.13 | 0.18 | 4.58 |
| ASV13 | NA | NA | NA | 3.77 | 4.22 | 2.96 | 0.45 | 4.52 |
| ASV18 | Russulales | Stereaceae | Stereum | 4.15 | 3.04 | 2.74 | 0.18 | 4.44 |
| ASV19 | Saccharomycetales | Debaryomycetaceae | Scheffersomyces | 3.22 | 4.30 | 3.39 | 0.14 | 4.43 |
| ASV22 | Xylariales | Xylariaceae | Xylaria | 4.31 | 0.00 | 3.51 | 0.02 | 4.37 |
| ASV23 | Xylariales | Xylariaceae | Daldinia | 4.35 | 0.00 | 0.00 | 0.02 | 4.35 |
| ASV26 | Russulales | Stereaceae | Stereum | 2.09 | 3.06 | 4.15 | 0.07 | 4.32 |
| ASV27 | Polyporales | Steccherinaceae | Antrodiella | 3.23 | 4.28 | 0.90 | 0.02 | 4.31 |
| ASV28 | Pertusariales | Pertusariaceae | Pertusaria | 4.06 | 3.01 | 3.69 | 0.22 | 4.30 |
| ASV35 | Polyporales | Polyporaceae | Fomes | 3.70 | 2.94 | 3.97 | 0.04 | 4.18 |
| ASV41 | Agaricales | Tricholomataceae | Mycena | 0.00 | 1.08 | 4.02 | 0.05 | 4.11 |
| ASV43 | Pleosporales | Amorosiaceae | Angustimassarina | 1.65 | 4.04 | 3.00 | 0.16 | 4.08 |
| ASV45 | Helotiales | Helotiaceae | Scytalidium | 4.03 | 0.48 | 1.62 | 0.05 | 4.07 |
| ASV46 | Atractiellales | Atractiellales_fam_Incertae_sedis | Helicogloea | 3.09 | 3.91 | 3.05 | 0.04 | 4.04 |
| ASV53 | Polyporales | Polyporaceae | Fomes | 3.61 | 1.91 | 3.77 | 0.03 | 4.00 |
track_sequences_samples_clustersError: objet 'track_sequences_samples_clusters' introuvable
track_by_samplesError: objet 'track_by_samples' introuvable
Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data_final/information_run.txt .
sessionInfo()R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] MiscMetabar_0.9.3 purrr_1.0.2 dplyr_1.1.4 dada2_1.32.0
[5] Rcpp_1.0.13 ggplot2_3.5.1 phyloseq_1.48.0 targets_1.8.0
[9] knitr_1.48
loaded via a namespace (and not attached):
[1] bitops_1.0-9 deldir_2.0-4
[3] gridExtra_2.3 permute_0.9-7
[5] rlang_1.1.4 magrittr_2.0.3
[7] ade4_1.7-22 matrixStats_1.4.1
[9] compiler_4.4.1 mgcv_1.9-1
[11] png_0.1-8 callr_3.7.6
[13] vctrs_0.6.5 reshape2_1.4.4
[15] stringr_1.5.1 pwalign_1.0.0
[17] pkgconfig_2.0.3 crayon_1.5.3
[19] fastmap_1.2.0 backports_1.5.0
[21] XVector_0.44.0 utf8_1.2.4
[23] Rsamtools_2.20.0 rmarkdown_2.28
[25] UCSC.utils_1.0.0 ps_1.8.0
[27] xfun_0.48 cachem_1.1.0
[29] zlibbioc_1.50.0 GenomeInfoDb_1.40.1
[31] jsonlite_1.8.9 biomformat_1.32.0
[33] rhdf5filters_1.16.0 DelayedArray_0.30.1
[35] Rhdf5lib_1.26.0 BiocParallel_1.38.0
[37] jpeg_0.1-10 parallel_4.4.1
[39] cluster_2.1.6 R6_2.5.1
[41] bslib_0.8.0 RColorBrewer_1.1-3
[43] stringi_1.8.4 jquerylib_0.1.4
[45] GenomicRanges_1.56.1 SummarizedExperiment_1.34.0
[47] iterators_1.0.14 IRanges_2.38.1
[49] Matrix_1.7-0 splines_4.4.1
[51] igraph_2.0.3 tidyselect_1.2.1
[53] viridis_0.6.5 rstudioapi_0.16.0
[55] abind_1.4-8 yaml_2.3.10
[57] vegan_2.6-8 codetools_0.2-20
[59] hwriter_1.3.2.1 processx_3.8.4
[61] lattice_0.22-6 tibble_3.2.1
[63] plyr_1.8.9 Biobase_2.64.0
[65] withr_3.0.1 ShortRead_1.62.0
[67] evaluate_1.0.0 survival_3.7-0
[69] RcppParallel_5.1.9 formattable_0.2.1
[71] Biostrings_2.72.1 pillar_1.9.0
[73] BiocManager_1.30.25 MatrixGenerics_1.16.0
[75] DT_0.33 renv_1.0.9
[77] foreach_1.5.2 stats4_4.4.1
[79] generics_0.1.3 rprojroot_2.0.4
[81] S4Vectors_0.42.1 munsell_0.5.1
[83] scales_1.3.0 base64url_1.4
[85] glue_1.8.0 tools_4.4.1
[87] interp_1.1-6 data.table_1.16.0
[89] GenomicAlignments_1.40.0 visNetwork_2.1.2
[91] rhdf5_2.48.0 grid_4.4.1
[93] tidyr_1.3.1 ape_5.8
[95] crosstalk_1.2.1 latticeExtra_0.6-30
[97] colorspace_2.1-1 nlme_3.1-166
[99] GenomeInfoDbData_1.2.12 cli_3.6.3
[101] fansi_1.0.6 viridisLite_0.4.2
[103] S4Arrays_1.4.1 gtable_0.3.5
[105] sass_0.4.9 digest_0.6.37
[107] BiocGenerics_0.50.0 SparseArray_1.4.8
[109] htmlwidgets_1.6.4 htmltools_0.5.8.1
[111] multtest_2.60.0 lifecycle_1.0.4
[113] here_1.0.1 httr_1.4.7
[115] secretbase_1.0.3 MASS_7.3-61
@online{taudière2024,
author = {Taudière, Adrien},
title = {Bioinformatics Pipeline Summary},
date = {2024-10-19},
langid = {en}
}